The newly reported figure for 2011 means the industry surpassed its 2009 target of reaching a £12.5 billion turnover by 2017 within two years.
Industry representatives Scotland Food & Drink has now set a new target of £16.5 billion turnover by 2017, including exports worth £7.1 billion.
Rural Affairs Secretary Richard Lochhead said: "Scotland's food and drink industry is a fantastic success story. I have no doubt that it has smashed its turnover target six years early because of the high-quality products and dedication of those working in the sector.
"I have always believed that our food and drink sector is the best in the world, thanks to our fantastic natural larder, iconic products, strong global brands, excellent provenance credentials and industry innovation.
"Today's figures, and last week's Bank of Scotland prediction of thousands of new jobs being created in the sector, demonstrate the strength of Scottish food and drink as an economic driver for Scotland. We have worked extremely hard to grow the sector, connect with existing and emerging markets and grow interest in our fantastic natural larder far and wide.
"But the industry is not going to rest on its laurels. Even now, higher, more ambitious targets have been set and I look forward to working with the Scottish food and drink sector as it strives to achieve more historic high sales."
Chief executive of Scotland Food and Drink James Withers said: "Reaching a turnover of over £13 billion annually is a tremendous result, beating our target six years early. This result is the product of ambition and partnership. After a period of flat growth up to 2007, we believed we could take the industry to a new level. The industry has worked collaboratively together to do this and government has worked in partnership with us to deliver.
"It is particularly appropriate that we announce this success and launch a new target during Scottish Food & Drink Fortnight. We're now committed to push on from here and believe we have the potential to reach £16.5 billion in turnover by 2017.
"Achieving this ambition means both building further business across the UK and, crucially, transforming our export activity and breaking into new markets."
Anne MacColl, chief executive of Scottish Development International which promotes global trade, said: "Scotland's food and drink industry has a great deal to offer the world: our wonderful natural assets, a clean environment and passionate producers.
"Today's figures demonstrate the ambition and capability of Scottish companies and reflect the collaboration between those producers, industry bodies and government. We have the right environment here for businesses to grow internationally and increase production.
"Food and drink is Scotland's top export industry and I am delighted to see it forging ahead with even more ambitious targets. Iconic products such as whisky, salmon, beef and shortbread, our strong global brands and our excellent provenance credentials will ensure that Scottish produce continues to command a strong premium position in UK and international markets.
"My message to Scottish food and drink companies of all sizes is that there is huge opportunity and we want to work with those already exporting and actively support those who have yet to export to take the step into new markets."
The Scotch Whisky Association (SWA) said: "With Scotch whisky exports accounting for around 80% of all Scottish food and drink exports, the industry intends to play its part in growing exports and is investing £2 billion over the next three to four years in new distilleries and warehousing to meet the global demand for Scotch whisky.
"Last week the SWA announced an 11% rise in the value of Scotch whisky exports for the first half of 2013 to £1,987 million."